The aim of this work was to study the effect of dairy system and individual cow-related factors on the volatile fingerprint of a large number of individual model cheeses analyzed by proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS). A total of 1,075 model cheeses were produced using milk samples collected from individual Brown Swiss cows reared in 72 herds located in mountainous areas of Trento province (Italy). The herds belonged to 5 main dairy systems ranging from traditional to modern and the cows presented different daily milk yields (24.6 ± 7.9 kg × d(-1)), stages of lactation (199 ± 138 d in milk), and parities (2.7 ± 1.8). The PTR-ToF-MS revealed 619 peaks, of which the 240 most intense were analyzed, and 61 of these were tentatively attributed to relevant volatile organic compounds on the basis of their fragmentation patterns and data from the literature. Principal component analysis was used to convert the multiple responses characterizing the PTR-ToF-MS spectra into 5 synthetic variables representing 62% of the total information. These principal components were related to groups of volatile compounds tentatively attributed to different peaks and used to investigate the relationship of the volatile compound profile obtained by PTR-ToF-MS to animal and farm characteristics. Lactation stage is related to 4 principal components which brought together 52.9% of the total variance and 57.9% of the area of analyzed peaks. In particular, 2 principal components were positively related to peaks tentatively attributed to aldehydes and ketones and negatively related to alcohols, esters, and acids, which displayed a linear increase during lactation. The second principal component was affected by dairy system; it was higher in the modern system in which cows received total mixed rations. The third principal component was positively related to daily milk production. In summary, we report the first application of this innovative, high-throughput technique to study the effects of dairy system and individual animal factors on volatile organic compounds of model cheeses. Individual cheesemaking procedures together with this spectrometric technique open new avenues for genetic selection of dairy species with respect to both milk and cheese quality.